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Kaleidoscope 4.1.0 Documentation

© 2017 Wildlife Acoustics, Inc. All Rights Reserved.

Please be sure to see our tutorial videos at http://www.wildlifeacoustics.com/support/tutorial-videos

For support, please contact support2017@wildlifeacoustics.com 1

Contents

Overview ...................................................................................................................................................... 4

Global Analysis Modes: Bats or Non-bats? .......................................................................................... 4

Batch

capabilities .................................................................................................................................... 4

Kaleidoscope Viewer ............................................................................................................................... 5

File Conversion............................................................................................................................................ 5

File Types ................................................................................................................................................. 5

Batch File Conversion ............................................................................................................................. 6

Choose the input files you wish to convert: ...................................................................................... 6

Choose the output formats you wish to convert to: ......................................................................... 7

Caveats ................................................................................................................................................. 8

Running the batch ............................................................................................................................... 8

File Naming Conventions ....................................................................................................................... 9

Filtering Noise Files (Bat Analysis Mode only) ........................................................................................ 9

Extracting GPS Tracks ............................................................................................................................. 10

Meta Data .................................................................................................................................................. 11

Kaleidoscope Meta Data ....................................................................................................................... 11

Mapping AnalookW Meta Data

to Kaleidoscope ............................................................................... 12

Adding Field Notes to Output Files ..................................................................................................... 13

Automatic Identification for Bats ............................................................................................................ 13

Output Summary File (idsummary.csv) ............................................................................................. 14

Output Identification File (id.csv) ....................................................................................................... 15

Explaining Maximum Likelihood Estimators (MLE) and P-values used in Kaleidoscope Classifiers

.................................................................................................................................................................... 18

Kaleidoscope Viewer ................................................................................................................................. 20

The Waveform Plot ............................................................................................................................... 20

The Spectrogram Plot ........................................................................................................................... 20

Shared Waveform and Spectrogram Controls ................................................................................... 22

Spectral Analysis ................................................................................................................................... 22

Playback ................................................................................................................................................. 24

Playback to a file ................................................................................................................................... 24

Saving a screenshot ............................................................................................................................... 24

2

Time Expansion ..................................................................................................................................... 24

Automatic Identification and Cluster Assignment............................................................................. 24

File and Folder Navigation ................................................................................................................... 25

Meta Data .............................................................................................................................................. 25

Results Table ......................................................................................................................................... 26

Settings ................................................................................................................................................... 27

Color Settings ........................................................................................................................................ 27

FFT Settings .......................................................................................................................................... 27

Keyboard Shortcuts .............................................................................................................................. 28

Cluster Analysis ........................................................................................................................................ 28

Clustering Modes .................................................................................................................................. 28

Scan and

Cluster Recordings ............................................................................................................... 29

Re-scan recordings and edited cluster.csv .......................................................................................... 29

Use existing .kcs file to sort new recordings ....................................................................................... 29

Overview of the Clustering Algorithm ................................................................................................ 29

Signal Detection and Feature Extraction ........................................................................................ 29

Hidden Markov Model ..................................................................................................................... 30

Fisher Scores ...................................................................................................................................... 30

Clustering........................................................................................................................................... 30

Pair-wise classifiers ........................................................................................................................... 30

Clustering Parameters .......................................................................................................................... 31

Parameters in the Cluster Analysis tab ........................................................................................... 31

Cluster Results Table ............................................................................................................................ 32

Noise Analysis Module .............................................................................................................................. 34

Noise Module Requirements ................................................................................................................ 34

Supported Measurements .................................................................................................................... 34

Configuring the Noise Analysis Module .............................................................................................. 35

Noise Analysis Module

Outputs ........................................................................................................... 36

Use of Meta Data ................................................................................................................................... 37

Kaleidoscope Release Notes 4.1.0............................................................................................................. 38

3

Overview

Kaleidoscope is

a collection of tools for the efficient processing of acoustic and ultrasonic recordings. Some of these tools are licensed separately. Mac OS X users should use "Control-Click" where these instructions refer to "Right-Click". Kaleidoscope retains most of its settings and writes them to a file "kaleidoscope.ini" in the user's

data directory (operating system specific). Before processing a batch of files, a copy of this file is

written to the "settings.ini" in the output directory. You can load a settings fil e or restore default settings from the "File->Load Settings..." and "File->Set Defaults" menus.

Global Analysis Modes: Bats or Non-bats?

Kaleidoscope has several settings and parameters that are specific to past and present conventions for recording bats (e.g. time expansion and zero crossing) that are not suitable for the conventions used to analyze other kinds of audio recordings. The first time you launch this version of Kaleidoscope, or after setting defaults, you will be asked to choose either "Bat Analysis Mode" or "Non-bats Analysis Mode" as your preferred analysis mode. You can also change your preference at any time using the control at the top left of the control panel. Many of Kaleidoscope's features and settings are only available in one of these two modes. Controls for features that are not available for the selected mode are disabled and greyed out.

Batch capabilities

In a single batch operation, Kaleidoscope can perform several tasks in parallel:

Convert audio file formats

o .wac from Wildlife Acoustics compressed format o .wav from or to Waveform Audio File Format o .??# or .zc from or to AnaLookW zero crossing sequence file format (bats only) o Support for both time-expanded (bats only) and normal speed .wavfiles o Support for breaking large files into smaller pieces o Support for splitting multi-channel recordings into multiple single channel recordings (note Kaleidoscope only supports up to two ch annels at this time) Add field notes to meta data in output files and extract meta data from files into output meta.csv Filter noise files detects and removes or segregates files containing only noise (bats only) Extract GPS metadata from files to produce .csv or .kml Automatic Identification for Bats of files to species and generate files suitable for creating pivot table reports (bats only, requires Kaleidoscope Pro or region -specific classifier license). Noise analysis measures signal levels in recordings using third octave bands and various weighting standards (non-bats only, requires Kaleidoscope Pro or noise analysis license). 4 Cluster analysis for detecting and sorting biological vocalizations in recordings into clusters by similarity and buildng customized classifiers (requires Kaleidoscope Pro license) Kaleidoscope runs in parallel during batch processing by dividing work into multiple threads to take advantage of computers with multiple processing cores. By default, Kaleidoscope will try to maximize utilization by using a number of threads equal to the number of available cores, plus one. Memory usage will also grow proportionally with the number of threads utilized. You can adjust the number of threads used by Kaleidoscope by using the pull-down in the upper right corner of the control panel e.g. "Use 3/5 compute resources". This may be necessary on a machine with limited memory available or desireable if you want to perform other tasks while

Kaleidoscope is running in the background.

Kaleidoscope Viewer

In addition, with

Kaleidoscope Viewer, you can:

View spectrograms by opening individual full spectrum or zero crossing files Take cursor measurements and view bat call parameters

Analyze and export spectral data

Add or edit meta data (e.g. field notes and manual classifications) to files Quickly review and manually verify automatic identifications Listen to or save .wav files applying bandpass filtering, speed and amplitude adjustments.

File Conversion

Kaleidoscope can convert a batch of input files recorded in a variety of in put formats to output files in a variety of output formats. This feature is available at no charge.

File Types

.wac Wildlife Acoustics Compressed Format The .wac or Wildlife Acoustics Audio Compression format is a legacy proprietary audio format produced by Song Meter and Echo Meter recorders. A .wac file may contain one or more channels (mono or stereo recordings), and these recordings may be either continuous or triggered. Triggered recordings are used for ultrasonic work (e.g. recording bats) where only periods of detected activity (a triggered event or "bat pass") are recorded. A triggered .wac file may contain several triggered events as they are detected independently on each channel. In addition to acoustic data, .wac files may contain GPS track information when created by GPS-enabled recorders. .wav Waveform Audio File Format 5 The .wav format is a defacto standard developed by IBM and Microsoft for representing multi -channel audio recordings. There are several flavors of .wav file formats that may util ize different forms of audio compression and meta data. Kaleidoscope supports only uncompressed 8 -bit and 16-bit Pulse Code Modulation (PCM) .wav files. Wildlife Acoustics has also defined a proprietary extension to the .wav file format to store metadata.

Time Expanded Files:

In "Bat Analysis Mode", the

.wav format described above may also represent time expanded recordings. Time expanded recordings are commonly used in ultrasonic work where the original recording is stretched through time by a constant fac tor effectively slowing it down such that ultrasonic signals are divided down into the audible range. This is accomplished by simply adjusting the sample rate of the recording. For example, if a recording is made at 384,000 samples per second, the sample rate in the file's metadata can be changed to 38,400 while keeping all the original audio samples. If we now play back this file at 38,400 samples per second, it will take ten times longer to play and the frequencies will have been divided down by a factor of ten times. Such a file would be said to have a time expansion factor of 10. With Kaleidoscope, you can specify an explicit expansion factor for input files, or you can use the "Auto" setting. The "Auto" setting assumes these are ultrasonic recordings, and uses a time expansion factor of one for sample rates greater than 96,000. Otherwise, a time expansion factor of ten will be used, unless a different time expansion factor is explicitly defined in the source file meta data. .??#, .zc AnalookW Zero Crossing Sequence File Format The .??# format is a proprietary format used in legacy zero-crossing bat detectors developed in the early 1990s by Chris Corben for Titley Electronics. These are not "recordings" in the conventional sense in that the original analog signal was not digitized and saved like they are in .wac and .wav files. Instead, the time between a number (division ratio) of sequential zero crossings is stored in the file. The original signal can not be reconstructed from this small amount of data. However, with sufficient signal-to- noise ratio, the dominant frequency sweep through time produced by the echolocation calls of bats can be represented. More recently, the .zc file extension is also used to represent these files.

Batch File Conversion

Choose the input files you wish to convert:

From the "Batch" tab on the Kaleidoscope control panel, set the "INPUTS" parameters found on the left hand side of the window: 6

1. Choose your "Input directory", a folder on your computer containing the input files you

wish to convert. Remember you are choosing a directory, not a file. On some operating systems, files in a given directory will not be shown, or will be grayed out. 2.

Check "Include subdirectories" if you want to convert files recursively in all the subfolders below the "Input directory" specified above. Otherwise only the files found in the "Input directory" will be converted and subfolders will be ignored.

3. Check "WAC files" if you want to convert from .wac files. 4. Check "WAV files" if you want to convert from .wav files. In "Bat Analysis Mode", you must also select the "Time expansion factor" used by the input files. A factor of "1" should be used for normal speed files. If the input .wav file was created by a time expansion bat detector, the time expansion factor should be set to the time expansion factor used to make the recording. The "Auto" setting can be used to automatically choose a time expansion factor of one for high-speed recordings (e.g. sample rates greater than 96 kHz) or ten for lower speed recordings (e.g. less than or equal to 96 kHz) unless an explicit time expansion factor can be found in the meta data. 5. In "Bat Analysis Mode", check "ZC files" if you want to convert from .??# and/or .zc files. 6. You can add comments and other textual information to the meta data in the output files by appending, prepending, or replacing any existing meta data. See

Meta data

for more information.

Choose the output formats you wish to convert to:

From the "Batch" tab on the Kaleidoscope control panel, set the "OUTPUTS" parameters found on the right hand side of the window: 1. Choose the output directory in which you want to write the output files. Note that this must not be under the input directory. If the input "Include subdirectories" is checked, output subfolders will be created mirroring the directory structure of the inputs. 2. You can optionally have Kaleidoscope arrange outputs into daily or nightly subfolders (if Kaleidoscope can determine the recording timestamp from the input filenames or metadata) by choosing "Daily" or "Nightly" for "Create subdirectories" Otherwise, you can specify "None". 3.

If you would like Kaleidoscope to break up long files into multiple short files, you can specify a value for "Split to max duration", otherwise leave this field blank.

4. Check "WAV files" if you wish to convert to .wav files. Check "Split channels" if you would like to separate each channel of a multi-channel input file into individual single- channel output files. In "Bat Analysis Mode", if you want to output time expanded files, you can specify a time expansion factor. For normal time files, use a factor of "1". 5. In "Bat Analysis Mode", check "ZC files" if you wish to convert to .??# files. You can specify the ":Division Ratio" to use. You can also check the "8.3 file names" to output files with the legacy 8.3 filename convention (note that 8.3 filename convention can only be performed if the input files have a compatible timest amp). Otherwise Kaleidoscope will use the suffix .00# or, if you check "Use .zc instead of .??#", Kaleidoscope will use the suffix .zc 7

Caveats

In "Bat Analysis Mode", there are a number of important caveats to keep in mind when converting files: 1. Converting from .??# or .zc zero crossing formats to .wav full spectrum formats is not possible to do accurately because zero crossing formats do not contain any amplitude or harmonic content information from the original recorded signal. Instead, Kaleidoscope uses sophisticated digital signal processing techniques to synthesize a full spectrum signal from the zero crossing data that simulates the frequency modulated signal through time, but with no harmonic structure and with uniform amplitude information. 2. Converting from .??# or .zc to .??# or .zc produces a copy of the original file and does not actually change the division ratio or split the recording into smaller pieces. 3. The .??# and .zc file format has a number of file size and duration limitations that are enforced. If converting from a longer .wav or .wac file, multiple .??# files may be produced to avoid exceeding these limits (15 second duration or 32KB filesize or 16K divided zero crossing points). 4. Converting from .wav or .wac full spectrum to .??# zero crossing uses digital signal processing controlled by additional parameters found in the "Signal Parameters" tab of the Kaleidoscope control panel. Zero crossing hardware technology has a disadvantage over full spectrum recording technology of approximately 20 dB in signal -to-noise ratio (SNR) because zero crossing hardware must overcome noise in the entire frequency bandwidth of interest while Fourier analysis of full spectrum signals must only overcome noise in a narrow frequency bin. Kaleidoscope implements p atented advanced signal processing algorithms for extracting zero crossing data from full spectrum recordings. These algorithms are enabled (by default, recommended) by checking the box "When zero crossing for conversion or analysis, enhace with advanced signal processing" in the "Signal Parameters" tab of the Kaleidoscope control panel. When turned off, the full spectrum input is band -pass filtered according to the frequency range specified by the "Signal of interest" described in the "Signal Parameters" tab and the resulting signal is converted to zero crossing without further enhancement. When turned on, Kaleidoscope further enhances the signal with noise reduction and echo cancellation techniques prior to zero crossing, but also removes echoes and fragmented calls. The result is a cleaner filtered zero crossing output that may detect weak signals that would have been missed or fragmented using conventional zero crossing hardware. On the other hand, some weaker or fragmented pulses remaining may be discarded. We recommend leaving this feature turned on, especially when using our "Auto ID for Bats"

Running the batch

Press the "Process files" button to run your batch. A progress bar will display estimated time remaining. Keep in mind that Kaleidoscope may be performing other tasks in parallel with file conversion such as filtering, GPS track extraction, automatic classification, noise analysis and cluster analysis. You should familiarize yourself with these features as they may affect the outputs. 8

File Naming Conventions

The Song Meter line of products use the following naming convention:

Prefix_ YYYYMMDD_hhmmss . extension

A "Prefix" may be optionally specified in the Song Meter configuration (typically to keep track of files from different Song Meters with different prefixes). If present, the prefix is prepended to the filename with an underscore character between the prefix and the year. The extension is either "wav" for a WAV file, "wac" for a WAC file, or "00#" or "zc" for a Zero crossing file.

On the

Echo Meter EM3, the file name convention is slightly different to accommodate an additional optional tag character (represented by "T" below). This may be included if one of the tag buttons (e.g. A, B, C, or D) is pressed during recording, or the special "N" tag used to mark

potential noise files. If no tag is present and the file is not a noise file, then the tag character is an

underscore. The file name looks like this:

Prefix_ T_YYYYMDD_hhmmss . extension

The output file name format will be in one of the following formats:

Prefix_ YYYYMMDD_hhmmss_mmm . extension

Prefix_ T_YYYYMMDD_hhmmss_mmm . extension

Prefix_ C_YYYYMMDD_hhmmss_mmm . extension

If an Echo Meter tag is specified, the second form is used with "T" representing the tag

If splitting

channels from stereo to two mono channels, the third form is used with "C" representing the channel number (0 = left, 1 = right). Otherwise the first form is used. In all these forms, an additional mmm is appended indicating the milliseconds offset. When converting files that are not in the Song Meter filename format, the original filename is preserved and appended with _C_sssss_mmm . extension.

Filtering Noise Files (Bat Analysis Mode

only)

During batch

file conversion, Kaleidoscope can analyze each output file looking for biological activity of interest and removing files containing only uninteresting signals such as ambient background noise, rain an d wind, or unwanted biological signals such as insects when trying to record bats. 9 Kaleidoscope looks for echolocation pulses of smooth continuous narrowband frequency sweeps characteristic of bats. On the "Signal Parameters" tab of the Kaleidoscope control panel, there are several parameters used to describe the signal of interest. As files are processed, Kaleidoscope decides if the file meets the criterion specified. If a file does not contain at least "Minimum number of pulses" that have frequencies and durations in the ranges specified, then the file is considered "noise". On the "Batch" tab of the Kaleidoscope control panel under "OUTPUTS", there is a pull-down to control noise filtering: 1. Disable noise filtering disables filtering of noise files. All files are processed even if no pulses are detected. 2. Delete noise files deletes any output files that are considered noise. 3.

Move noise files to NOISE subfolder moves any output files considered to be noise to a subfolder marked "NOISE" so the files can still be manually reviewed but are conveniently segregated from files more likely to contain good echolocation calls.

Useful tip: weak signals may cause a discontinuity in a detected syllable resulting in two or more smaller fragments. You may want to use smaller values for the minimum signal duration in order to consider these weaker signals as "interesting". Setting the minimum duration to 0ms will allow even the smallest pulses to be counted as long as they meet the frequency range requirements.

Extracting GPS Tracks

During batch

file conversion, the GPS track can be extracted from meta data found in the input files. To enable this feature, you can go to the "Batch" tab of the Kaleidoscope conrol panel and choose the GPS processing mode:

Extract GPS Disabled

Disables extraction of GPS metadata.

Extract GPS to CSV

Extract GPS data found in the metadata of input files and create a "gps.csv" file in the outpu t directory. Columns are created for DATE, TIME, LAT, LON, and NAME, where NAME is the filename of the corresponding output file or blank for waypoints. If waypoints are available (e.g. in a .WAC file), the frequency of waypoint extraction can be specified in seconds.

Extract GPS to KML

10 Extract GPS data found in the metadata of input files and create a "gps.km" file in the output directory. The KML file can be opened directly from Google Earth and have a placemark corresponding to each output file. If waypo ints are available (e.g. in a .WAC file), the frequency of waypoint extraction can be specified in seconds and are repesented as a path in the KML.

Meta Data

Meta data are bits of information embedded in an audio files that might be useful in the interpretation of the recordings. For example, meta data might describe the location, habitat, weather, and deployment details for a given recording session. Kaleidoscope enables the use of meta data embedded in audio files. For .wav files, Wildlife Acoustics defines a proprietary extension in which to store meta data. For .??# and .zc files, there are a number of fields defined for this purpose. Meta data can be viewed (and some fields can be edited) from the meta data control panel in

Kaleidoscope Viewer. This pan

el can be toggled between hidden and shown with the button.

Kaleidoscope Meta Data

Kaleidoscope makes use of the following meta data fields if available in the recording:

Voice note

An embedded audio notation such as those created by the Echo Meter Touch.

The icon

button will appear if a voice note is present, and clicking the button will play the voice note recording.

Prefix

The user-defined file prefix.

Model

The recorder model name.

Serial Number

The recorder serial number.

Firmware

The recorder firmware version.

11

Timestamp

The date and time a recording was made.

GPS Location

If a GPS receiver was attached to the recorder, the GPS coordinates corresponding to where the recording was made may be available. Notes Field notes created, edited and viewed by humans that could be used to describe the field and deployment conditions in great detail.

Auto Identification Results

The automatic identification made to species by Kaleidoscope's Auto ID for Bats

Manual Identification Results

The manually verified identification made to species by a human expert.

Microphone Sensitivity

Calibrated microphone sensitivities saved in the recorder and used by the noise analysis module

Mapping AnalookW Meta Data to Kaleidoscope

For .??# or .zc files manipulated by AnalookW software, there are several meta data fields mapped to and from Kaleidoscope meta data fields as follows:

AnalookW

Meta Data

Kaleidoscope Meta

Data

Additional Comments

Tape Notes A line in the Notes field that begins with "Tape: " Loc Notes A line in the Notes field that begins with "Location: " Spec Notes A line in the Notes field that begins with "Spec: "

Notes Notes Additional lines in the Notes field

Filetime Timestamp

Lat, Lon GPS Location

Species

Automatic

Identification

Results and Manual

The "Species" field in AnalookW is formatted as

"AUTOID (KS AUTOID,STATS)" or "MANUALID !(KS

AUTOID,STATS)" where AUTOID is the automatic

12

Identification

Results

classification, MANUALID is the manually verified classification, and STATS are Kaleidoscope statistics. Note that older versions of Kaleidoscope used "Kaleidoscope" instead of "KS" as shown above. This was shortened to allow for more available space in this field for other uses.

Adding Field Notes to Output Files

During batch

file conversion, Kaleidoscope can replace, append, or prepend field notes to the meta data in output files. On the "Batch" tab of the Kaleidoscope control panel at the bottom of the "INPUTS" section on the left, you can select from among "Append notes to output meta data", "Prepend notes to output meta data" or "Replace n otes in output meta data" and optionally type field notes into the text box below this choice. When you run the batch job, any notes provided will be added to any existing notes (depending on the choice specified) and written to the output files. Note that the original input files are not modified during batch processing. When outputting to .??# or .zc files, lines beginning with "Tape: ", "Location: " and "Spec: " are treated specially with the remainder of the line written to and replacing the corresponding AnalookW fields.

Automatic Identification for Bats

NOTICE: Automatic identification is not perfect and will result in false positive and false negative errors. Never rely solely on the output of this software to make land management decsions. The automa tic identicication is intended only as a suggestion to facilitate analysis, not to replace human expert vetting of calls. You must have a Kaleidoscope Pro license or region -specific classifier lisense to use the automatic identification feature. Wildlife Acoustics is building classifiers capable of fast and accurate identification to species. At this time, classifiers are offered for bats of North America, South and Central America, and Europe. Not all species are covered, and while our accuracy rates are impressive given the technical challenge, you should not rely solely on automatic classification results to draw conclusions. Our objective is to give you a tool to efficiently analyze a large quantity of data in a short period of time. Wildlife Acoustics h opes to continue expanding classification coverage to include other animals and geographic regions and to improve accuracy.

During batch

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